HTqPCR

DOI: 10.18129/B9.bioc.HTqPCR  

Automated analysis of high-throughput qPCR data

Bioconductor version: Release (3.16)

Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).

Author: Heidi Dvinge, Paul Bertone

Maintainer: Heidi Dvinge <hdvinge at fredhutch.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HTqPCR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HTqPCR")

 

PDF	R Script	qPCR analysis in R
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, DifferentialExpression, GeneExpression, MicrotitrePlateAssay, MultipleComparison, Preprocessing, QualityControl, Software, Visualization, qPCR
Version	1.52.0
In Bioconductor since	BioC 2.5 (R-2.10) (13.5 years)
License	Artistic-2.0
Depends	Biobase, RColorBrewer, limma
Imports	affy, Biobase, gplots, graphics, grDevices, limma, methods, RColorBrewer, stats, stats4, utils
LinkingTo
Suggests	statmod
SystemRequirements
Enhances
URL	http://www.ebi.ac.uk/bertone/software
Depends On Me
Imports Me	nondetects, unifiedWMWqPCR
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HTqPCR_1.52.0.tar.gz
Windows Binary	HTqPCR_1.52.0.zip
macOS Binary (x86_64)	HTqPCR_1.52.0.tgz
macOS Binary (arm64)	HTqPCR_1.52.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HTqPCR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HTqPCR
Bioc Package Browser	https://code.bioconductor.org/browse/HTqPCR/
Package Short Url	https://bioconductor.org/packages/HTqPCR/
Package Downloads Report	Download Stats